Better representing of Tumor_Seq_Allele

genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API

MIT License

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Open leexgh opened 5 years ago

leexgh commented 5 years ago

For example,

	Chromosome	Start_Position	End_Position	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	NCBI_Build
input	11	108151707	108151707	T	TA		37
output	11	108151707	108151708	-	TA	A	37

The Tumor_Seq_Allele2 can also represent the zygosity, so maybe we could consider a better way to show those fields?

jjgao commented 5 years ago

Discussed with @inodb. Here are some notes:

We think that it's not a good idea to override the original file. It would good to keep the original file at least.
This particular output is actually wrong -- one allele now becomes two alleles and the first one shouldn't be there.
We are only importing Tumor_Seq_Allele2 only so the data in our database is not wrong.
Maybe we should not try to curate Tumor_Seq_Allele1 at all?